Contemporaneous treatment of malocclusions concerns about the effect of the muscular activity in the occlusion. Treatment of malocclusion involves dental alignment, jaw repositioning, stabilization of the activity of the masticatory muscles, the muscles of the tongue and the muscles of the cheeks and lips in order to achieve a balance between the forces delivered on the arches and teeth by all the muscles involved in oral functions. Any alteration in the muscular activity of these muscles is what the authors term “soft tissue dysfunction”. It is necessary that dentists treating malocclusion be aware of this dysfunction and acquire the required knowledge to recognize it. The current paper reviews the biology of the muscles of the cheeks, lips and tongue and how their action may affect the occlusion. The goals for an ideal treatment of malocclusions and how appliances based in the oral physiology must be designed to get better success and more stability in the treatment are also discussed.